Merge pull request #119 from Plant-Food-Research-Open/updates

Updated modules and sub workflows
Plant-Food-Research-Open · Jul 29, 2024 · 41e6331 · 41e6331
2 parents 4268dea + c5d285e
commit 41e6331
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Showing 145 changed files with 6,893 additions and 1,333 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -25,20 +25,6 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
-# These files are edited and tested upstream in pfr/modules
-[/modules/pfr/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-[/subworkflows/pfr/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-
 # These files are edited and tested upstream in gallvp/modules
 [/modules/gallvp/**]
 charset = unset

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -51,27 +51,7 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: |
-          nf-core -l lint_log.txt lint \
-            --dir ${GITHUB_WORKSPACE} \
-            --markdown lint_results.md \
-            --key actions_ci \
-            --key actions_schema_validation \
-            --key base_config \
-            --key files_exist \
-            --key files_unchanged \
-            --key merge_markers \
-            --key modules_config \
-            --key multiqc_config \
-            --key nextflow_config \
-            --key nfcore_yml \
-            --key pipeline_name_conventions \
-            --key pipeline_todos \
-            --key readme \
-            --key schema_description \
-            --key schema_lint \
-            --key schema_params \
-            --key system_exit
+        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -13,7 +13,6 @@ lint:
     - docs/README.md
     - .github/PULL_REQUEST_TEMPLATE.md
     - .github/CONTRIBUTING.md
-    - .github/workflows/linting.yml
     - .github/workflows/branch.yml
     - LICENSE
   nextflow_config:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,17 +3,17 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.1.0+dev - [29-July-2024]
+## v2.1.0+dev - [30-July-2024]
 
 ### `Added`
 
 1. Created summary presence/absence tables for NCBI FCS modules [#88](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/88)
 2. Added min. system requirements [#91](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/91)
-3. Updated modules: `UNTAR`, `MERYL_COUNT`, `GUNZIP`, `MINIMAP2_ALIGN`
-4. Added a test to verify the fix for the bug which resulted in a pipeline crash for assemblies without LTRs
-5. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
-6. Updated `SYRI` to 1.7.0 [#104](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/104)
-7. Added a script to automatically check for updates on GitHub/GitLab and post issues
+3. Added a test to verify the fix for the bug which resulted in a pipeline crash for assemblies without LTRs
+4. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
+5. Updated `SYRI` to 1.7.0 [#104](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/104)
+6. Added a script to automatically check for updates on GitHub/GitLab and post issues
+7. Updated modules: `UNTAR`, `MERYL_COUNT`, `GUNZIP`, `MINIMAP2_ALIGN`, `FASTQC`
 
 ### `Fixed`
 
@@ -35,6 +35,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 1. Changed default branch name from `master` to `main` in nf-core template files
 2. Moved `version_check.sh` to `.github/version_checks.sh`
 3. Moved `docs/contributors.sh` to `.github/contributors.sh`
+4. Removed dependency on <https://github.com/PlantandFoodResearch/nxf-modules.git>
+5. Replaced `nf-core/fastq_trim_fastp_fastqc` with `nf-core/fastq_fastqc_umitools_fastp` which has nf-test unit tests
 
 ## v2.0.0 - [04-June-2024]
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -282,23 +282,23 @@ process {
         ]
     }
 
-    withName: FASTQC_RAW {
+    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
         publishDir = [
             path: { "${params.outdir}/hic/fastqc_raw" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
         ]
     }
 
-    withName: FASTQC_TRIM {
+    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
         publishDir = [
             path: { "${params.outdir}/hic/fastqc_trim" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
         ]
     }
 
-    withName: FASTP {
+    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
         ext.args = params.hic_fastp_ext_args
         publishDir = [
             path: { "${params.outdir}/hic/fastp" },

diff --git a/modules.json b/modules.json
@@ -5,148 +5,133 @@
         "https://github.com/GallVp/nxf-components.git": {
             "modules": {
                 "gallvp": {
-                    "cat/cat": {
-                        "branch": "main",
-                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "custom/restoregffids": {
-                        "branch": "main",
-                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "custom/shortenfastaids": {
-                        "branch": "main",
-                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "ltrfinder": {
-                        "branch": "main",
-                        "git_sha": "db7fb043c5557cf06a49a1edbed16e282a7dffb2",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "ltrharvest": {
-                        "branch": "main",
-                        "git_sha": "db7fb043c5557cf06a49a1edbed16e282a7dffb2",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "ltrretriever/lai": {
-                        "branch": "main",
-                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "ltrretriever/ltrretriever": {
-                        "branch": "main",
-                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "seqkit/seq": {
-                        "branch": "main",
-                        "git_sha": "8ec55a2c8e4ce3af070393768f6c2c57f5c34076",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "syri": {
-                        "branch": "main",
-                        "git_sha": "836bb223521eeaa08d65c1b7f4b82be1272a1964",
-                        "installed_by": ["modules"]
-                    }
-                }
-            },
-            "subworkflows": {
-                "gallvp": {
-                    "fasta_ltrretriever_lai": {
-                        "branch": "main",
-                        "git_sha": "8ec55a2c8e4ce3af070393768f6c2c57f5c34076",
-                        "installed_by": ["subworkflows"]
-                    }
-                }
-            }
-        },
-        "https://github.com/PlantandFoodResearch/nxf-modules.git": {
-            "modules": {
-                "pfr": {
                     "busco/busco": {
                         "branch": "main",
-                        "git_sha": "c3ef9317fe867609f5927588fbf17e3c3ebf389c",
+                        "git_sha": "ab92c438688c1f4a3753b65914bfd2e6319cebb2",
                         "installed_by": ["fasta_gxf_busco_plot"]
                     },
                     "busco/generateplot": {
                         "branch": "main",
-                        "git_sha": "c3ef9317fe867609f5927588fbf17e3c3ebf389c",
+                        "git_sha": "ab92c438688c1f4a3753b65914bfd2e6319cebb2",
                         "installed_by": ["fasta_gxf_busco_plot"]
                     },
                     "bwa/index": {
                         "branch": "main",
-                        "git_sha": "d158062346649b5d55bccef77f4bbd0468760aff",
+                        "git_sha": "3cba9e138cf07f2db778a7ad6aae0ab707948c74",
                         "installed_by": ["fastq_bwa_mem_samblaster"]
                     },
                     "bwa/mem": {
                         "branch": "main",
-                        "git_sha": "d158062346649b5d55bccef77f4bbd0468760aff",
+                        "git_sha": "3cba9e138cf07f2db778a7ad6aae0ab707948c74",
                         "installed_by": ["fastq_bwa_mem_samblaster"]
                     },
+                    "cat/cat": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
                     "custom/relabelfasta": {
                         "branch": "main",
-                        "git_sha": "0421bdeb1d7a71dce12e0af7dc18aea26e548074",
+                        "git_sha": "775762619b57101ca800269b6ecda0b915fb9913",
                         "installed_by": ["modules"]
                     },
+                    "custom/restoregffids": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "custom/shortenfastaids": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
                     "gffread": {
                         "branch": "main",
-                        "git_sha": "c3ef9317fe867609f5927588fbf17e3c3ebf389c",
+                        "git_sha": "c04bf39d67027e044a6eaed0b7b0439fd8866fc7",
                         "installed_by": ["fasta_gxf_busco_plot"]
                     },
                     "gt/gff3": {
                         "branch": "main",
-                        "git_sha": "84f31d4be03e2ae6bee8e0b9fdea466be8e997bb",
+                        "git_sha": "c68acf8c8993f85be6e417d0db1bbf3a919f9226",
                         "installed_by": ["gff3_gt_gff3_gff3validator_stat"]
                     },
                     "gt/gff3validator": {
                         "branch": "main",
-                        "git_sha": "84f31d4be03e2ae6bee8e0b9fdea466be8e997bb",
+                        "git_sha": "49bbf276b8aeda94bf69a982cdb6d68d7dc5ea4e",
                         "installed_by": ["gff3_gt_gff3_gff3validator_stat"]
                     },
                     "gt/stat": {
                         "branch": "main",
-                        "git_sha": "ffd39a616c84c814fdfb2a865e9fbbb06e5343d9",
-                        "installed_by": ["gff3_gt_gff3_gff3validator_stat", "modules"]
+                        "git_sha": "c68acf8c8993f85be6e417d0db1bbf3a919f9226",
+                        "installed_by": ["gff3_gt_gff3_gff3validator_stat"]
                     },
-                    "merqury/hapmers": {
+                    "ltrfinder": {
                         "branch": "main",
-                        "git_sha": "46b70684b6ae0ac60cae154c61796b293707db64",
-                        "installed_by": ["modules"]
+                        "git_sha": "db7fb043c5557cf06a49a1edbed16e282a7dffb2",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "ltrharvest": {
+                        "branch": "main",
+                        "git_sha": "db7fb043c5557cf06a49a1edbed16e282a7dffb2",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "ltrretriever/lai": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "ltrretriever/ltrretriever": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
                     },
                     "plotsr": {
                         "branch": "main",
-                        "git_sha": "0413d9b25b127f1c705349fb42de8ff54e83e1e9",
+                        "git_sha": "665454056d9cc2a1e1a392505ca8bf975ae1b711",
                         "installed_by": ["modules"]
                     },
                     "samblaster": {
                         "branch": "main",
-                        "git_sha": "10b046eaac396f279c08e7e2bb067482ccd9c74e",
+                        "git_sha": "53518187fb1f596f4779da061cd35ce9f973c06e",
                         "installed_by": ["fastq_bwa_mem_samblaster"]
                     },
                     "samtools/faidx": {
                         "branch": "main",
-                        "git_sha": "84f31d4be03e2ae6bee8e0b9fdea466be8e997bb",
+                        "git_sha": "c68acf8c8993f85be6e417d0db1bbf3a919f9226",
                         "installed_by": ["gff3_gt_gff3_gff3validator_stat"]
+                    },
+                    "seqkit/seq": {
+                        "branch": "main",
+                        "git_sha": "8ec55a2c8e4ce3af070393768f6c2c57f5c34076",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "syri": {
+                        "branch": "main",
+                        "git_sha": "836bb223521eeaa08d65c1b7f4b82be1272a1964",
+                        "installed_by": ["modules"]
                     }
                 }
             },
             "subworkflows": {
-                "pfr": {
+                "gallvp": {
                     "fasta_gxf_busco_plot": {
                         "branch": "main",
-                        "git_sha": "0e4afaff4964485d2d93f1115c5254a99765b9c1",
+                        "git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130",
+                        "installed_by": ["subworkflows"]
+                    },
+                    "fasta_ltrretriever_lai": {
+                        "branch": "main",
+                        "git_sha": "8ec55a2c8e4ce3af070393768f6c2c57f5c34076",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_bwa_mem_samblaster": {
                         "branch": "main",
-                        "git_sha": "d158062346649b5d55bccef77f4bbd0468760aff",
+                        "git_sha": "775762619b57101ca800269b6ecda0b915fb9913",
                         "installed_by": ["subworkflows"]
                     },
                     "gff3_gt_gff3_gff3validator_stat": {
                         "branch": "main",
-                        "git_sha": "84f31d4be03e2ae6bee8e0b9fdea466be8e997bb",
+                        "git_sha": "775762619b57101ca800269b6ecda0b915fb9913",
                         "installed_by": ["subworkflows"]
                     }
                 }
@@ -167,13 +152,13 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
-                        "installed_by": ["fastq_trim_fastp_fastqc"]
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+                        "installed_by": ["fastq_fastqc_umitools_fastp"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
-                        "installed_by": ["fastq_trim_fastp_fastqc"]
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+                        "installed_by": ["fastq_fastqc_umitools_fastp"]
                     },
                     "fcs/fcsadaptor": {
                         "branch": "master",
@@ -185,6 +170,11 @@
                         "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
                         "installed_by": ["modules"]
                     },
+                    "merqury/hapmers": {
+                        "branch": "master",
+                        "git_sha": "deadc7dfc8cd06aee6ab133df43242212ae1f8fb",
+                        "installed_by": ["modules"]
+                    },
                     "merqury/merqury": {
                         "branch": "master",
                         "git_sha": "5f7195c5a3e889a03c31c43aec72a65f8b1f9282",
@@ -202,7 +192,7 @@
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "e83b347b3e674de6bb1bb7bdf9b2674768c8e0fe",
+                        "git_sha": "a33ef9475558c6b8da08c5f522ddaca1ec810306",
                         "installed_by": ["modules"]
                     },
                     "seqkit/rmdup": {
@@ -245,6 +235,11 @@
                         "git_sha": "669a329f4aa37f5b7f03776c2ed1cd0ef122c626",
                         "installed_by": ["fasta_explore_search_plot_tidk"]
                     },
+                    "umitools/extract": {
+                        "branch": "master",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+                        "installed_by": ["fastq_fastqc_umitools_fastp"]
+                    },
                     "untar": {
                         "branch": "master",
                         "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
@@ -264,9 +259,9 @@
                         "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
                         "installed_by": ["subworkflows"]
                     },
-                    "fastq_trim_fastp_fastqc": {
+                    "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {

diff --git a/modules/pfr/busco/busco/environment.yml → modules/gallvp/busco/busco/environment.yml b/modules/pfr/busco/busco/environment.yml → modules/gallvp/busco/busco/environment.yml
diff --git a/modules/pfr/busco/busco/main.nf → modules/gallvp/busco/busco/main.nf b/modules/pfr/busco/busco/main.nf → modules/gallvp/busco/busco/main.nf
diff --git a/modules/pfr/busco/busco/meta.yml → modules/gallvp/busco/busco/meta.yml b/modules/pfr/busco/busco/meta.yml → modules/gallvp/busco/busco/meta.yml